Had you been using strict & warnings, perl would have informed you that "Multidimensional syntax $count_message[$hh1,$mm1] not supported".

In Perl multidimensional arrays (aka array of arrayrefs) are written:

$count_message[$hh1][$mm1]++;
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However, I think you'd be better off using hashes:

use Data::Dumper;

my %msg_rate = ('1', '00:00:00,284', '2', '00:00:00,462', '3', '01:01:
+00,462', '4', '00:02:00,462',
+'5', '01:03:00,462');

my %count_per_min;
while( my ($key1, $val1) = each(%msg_rate) ) {
    my ($hh1,$mm1,$ssms1) = split(/\:/,$val1);
    $count_per_min{"$hh1:$mm1"}++
}

print Dumper \%count_per_min;
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Output:

$VAR1 = {
          '00:00' => 2,
          '00:02' => 1,
          '01:03' => 1,
          '01:01' => 1
        };
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